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For: Vilas JL, Gómez-Blanco J, Conesa P, Melero R, Miguel de la Rosa-Trevín J, Otón J, Cuenca J, Marabini R, Carazo JM, Vargas J, Sorzano COS. MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps. Structure 2018;26:337-344.e4. [PMID: 29395788 DOI: 10.1016/j.str.2017.12.018] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/06/2017] [Accepted: 12/29/2017] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
1
Makino T, Kanada R, Mori T, Miyazono KI, Komori Y, Yanagisawa H, Takada S, Tanokura M, Kikkawa M, Tomishige M. Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping. J Cell Biol 2025;224:e202501253. [PMID: 40298806 PMCID: PMC12039583 DOI: 10.1083/jcb.202501253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 03/18/2025] [Accepted: 04/08/2025] [Indexed: 04/30/2025]  Open
2
Zhu H, Terashi G, Farheen F, Nakamura T, Kihara D. AI-based quality assessment methods for protein structure models from cryo-EM. Curr Res Struct Biol 2025;9:100164. [PMID: 39996138 PMCID: PMC11848767 DOI: 10.1016/j.crstbi.2025.100164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/23/2025] [Accepted: 01/29/2025] [Indexed: 02/26/2025]  Open
3
Jia H, Guan Z, Ding J, Wang X, Tian D, Zhu Y, Zhang D, Liu Z, Ma L, Yin P. Structural insight into PIF6-mediated red light signal transduction of plant phytochrome B. Cell Discov 2025;11:51. [PMID: 40404641 PMCID: PMC12098889 DOI: 10.1038/s41421-025-00802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Accepted: 04/27/2025] [Indexed: 05/24/2025]  Open
4
Ghanbarpour A, Telusma B, Powell BM, Zhang JJ, Bolstad I, Vargas C, Keller S, Baker TA, Sauer RT, Davis JH. An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. EMBO J 2025;44:2501-2513. [PMID: 40082723 PMCID: PMC12048511 DOI: 10.1038/s44318-025-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 12/13/2024] [Accepted: 02/28/2025] [Indexed: 03/16/2025]  Open
5
Tai MDS, Ochoa L, Flydal MI, Velasco-Carneros L, Muntaner J, Santiago C, Gamiz-Arco G, Moro F, Jung-Kc K, Gil-Cantero D, Marcilla M, Kallio JP, Muga A, Valpuesta JM, Cuéllar J, Martinez A. Structural recognition and stabilization of tyrosine hydroxylase by the J-domain protein DNAJC12. Nat Commun 2025;16:2755. [PMID: 40113792 PMCID: PMC11926245 DOI: 10.1038/s41467-025-57733-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/28/2025] [Indexed: 03/22/2025]  Open
6
Muenks A, Farrell DP, Zhou G, DiMaio F. Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.20.623795. [PMID: 39605546 PMCID: PMC11601544 DOI: 10.1101/2024.11.20.623795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
7
Gil-Cantero D, Mata CP, Valiente L, Rodríguez-Huete A, Valbuena A, Twarock R, Stockley PG, Mateu MG, Castón JR. Cryo-EM of human rhinovirus reveals capsid-RNA duplex interactions that provide insights into virus assembly and genome uncoating. Commun Biol 2024;7:1501. [PMID: 39537894 PMCID: PMC11561273 DOI: 10.1038/s42003-024-07213-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]  Open
8
Ghanbarpour A, Sauer RT, Davis JH. A proteolytic AAA+ machine poised to unfold protein substrates. Nat Commun 2024;15:9681. [PMID: 39516482 PMCID: PMC11549327 DOI: 10.1038/s41467-024-53681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024]  Open
9
Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024;20:1493-1504. [PMID: 38658656 PMCID: PMC11529724 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
10
Ghanbarpour A, Telusma B, Powell BM, Zhang JJ, Bolstad I, Vargas C, Keller S, Baker T, Sauer RT, Davis JH. An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.604662. [PMID: 39149393 PMCID: PMC11326279 DOI: 10.1101/2024.08.09.604662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
11
Li A, You T, Pang X, Wang Y, Tian L, Li X, Liu Z. Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Nat Commun 2024;15:5211. [PMID: 38890314 PMCID: PMC11189392 DOI: 10.1038/s41467-024-49532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024]  Open
12
Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024;384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
13
Jojoa-Cruz S, Dubin AE, Lee WH, Ward AB. Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli. eLife 2024;12:RP93147. [PMID: 38592763 PMCID: PMC11003742 DOI: 10.7554/elife.93147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]  Open
14
Sanchez-Garcia R, Gaullier G, Cuadra-Troncoso JM, Vargas J. Cryo-EM Map Anisotropy Can Be Attenuated by Map Post-Processing and a New Method for Its Estimation. Int J Mol Sci 2024;25:3959. [PMID: 38612769 PMCID: PMC11012471 DOI: 10.3390/ijms25073959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]  Open
15
Liu G, Niu T, Qiu M, Zhu Y, Sun F, Yang G. DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning. Nat Commun 2024;15:2090. [PMID: 38453943 PMCID: PMC11258139 DOI: 10.1038/s41467-024-46041-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/09/2024]  Open
16
Sievers K, Neumann P, Sušac L, Da Vela S, Graewert M, Trowitzsch S, Svergun D, Tampé R, Ficner R. Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Structure 2024;32:316-327.e5. [PMID: 38181786 DOI: 10.1016/j.str.2023.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
17
Jojoa-Cruz S, Dubin AE, Lee WH, Ward A. Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560740. [PMID: 37873218 PMCID: PMC10592937 DOI: 10.1101/2023.10.03.560740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
18
Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCRJ 2024;11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
19
Jojoa-Cruz S, Burendei B, Lee WH, Ward AB. Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain. Structure 2024;32:157-167.e5. [PMID: 38103547 PMCID: PMC10872982 DOI: 10.1016/j.str.2023.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/29/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
20
Ghanbarpour A, Sauer RT, Davis JH. A proteolytic AAA+ machine poised to unfold a protein substrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571662. [PMID: 38168193 PMCID: PMC10760120 DOI: 10.1101/2023.12.14.571662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
21
Fernandez-Gimenez E, Carazo JM, Sorzano COS. Local defocus estimation in single particle analysis in cryo-electron microscopy. J Struct Biol 2023;215:108030. [PMID: 37758154 DOI: 10.1016/j.jsb.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023]
22
Semchonok DA, Kyrilis FL, Hamdi F, Kastritis PL. Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote. J Struct Biol X 2023;8:100094. [PMID: 37638207 PMCID: PMC10451023 DOI: 10.1016/j.yjsbx.2023.100094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023]  Open
23
Fernández-Giménez E, Martínez MM, Marabini R, Strelak D, Sánchez-García R, Carazo JM, Sorzano COS. A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis. J Struct Biol 2023;215:108024. [PMID: 37704013 DOI: 10.1016/j.jsb.2023.108024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
24
Ghanbarpour A, Cohen SE, Fei X, Kinman LF, Bell TA, Zhang JJ, Baker TA, Davis JH, Sauer RT. A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation. Nat Commun 2023;14:7281. [PMID: 37949857 PMCID: PMC10638403 DOI: 10.1038/s41467-023-43145-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2023] [Indexed: 11/12/2023]  Open
25
Abbasi Yeganeh F, Rastegarpouyani H, Li J, Taylor KA. Structure of the Drosophila melanogaster Flight Muscle Myosin Filament at 4.7 Å Resolution Reveals New Details of Non-Myosin Proteins. Int J Mol Sci 2023;24:14936. [PMID: 37834384 PMCID: PMC10573858 DOI: 10.3390/ijms241914936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023]  Open
26
Wright KM, DiNapoli SR, Miller MS, Aitana Azurmendi P, Zhao X, Yu Z, Chakrabarti M, Shi W, Douglass J, Hwang MS, Hsiue EHC, Mog BJ, Pearlman AH, Paul S, Konig MF, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen. Nat Commun 2023;14:5063. [PMID: 37604828 PMCID: PMC10442379 DOI: 10.1038/s41467-023-40821-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 08/10/2023] [Indexed: 08/23/2023]  Open
27
Conesa P, Fonseca YC, Jiménez de la Morena J, Sharov G, de la Rosa-Trevín JM, Cuervo A, García Mena A, Rodríguez de Francisco B, del Hoyo D, Herreros D, Marchan D, Strelak D, Fernández-Giménez E, Ramírez-Aportela E, de Isidro-Gómez FP, Sánchez I, Krieger J, Vilas JL, del Cano L, Gragera M, Iceta M, Martínez M, Losana P, Melero R, Marabini R, Carazo JM, Sorzano COS. Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology. BIOLOGICAL IMAGING 2023;3:e13. [PMID: 38510163 PMCID: PMC10951921 DOI: 10.1017/s2633903x23000132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 03/22/2024]
28
Lunin VY, Lunina NL, Urzhumtsev AG. Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation. Curr Res Struct Biol 2023;6:100102. [PMID: 37424695 PMCID: PMC10329102 DOI: 10.1016/j.crstbi.2023.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023]  Open
29
Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun 2023;14:3439. [PMID: 37301887 PMCID: PMC10257715 DOI: 10.1038/s41467-023-39037-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]  Open
30
He J, Li T, Huang SY. Improvement of cryo-EM maps by simultaneous local and non-local deep learning. Nat Commun 2023;14:3217. [PMID: 37270635 DOI: 10.1038/s41467-023-39031-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/25/2023] [Indexed: 06/05/2023]  Open
31
Matsumoto S, Ishida S, Terayama K, Okuno Y. Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations. Biophys Physicobiol 2023;20:e200022. [PMID: 38496243 PMCID: PMC10941960 DOI: 10.2142/biophysico.bppb-v20.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/12/2023] [Indexed: 03/19/2024]  Open
32
Herreros D, Kiska J, Ramirez E, Filipovic J, Carazo JM, Sorzano COS. ZART: A novel multiresolution reconstruction algorithm with motion-blur correction for single particle analysis. J Mol Biol 2023;435:168088. [PMID: 37030648 DOI: 10.1016/j.jmb.2023.168088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/10/2023]
33
Dai M, Dong Z, Xu K, Cliff Zhang Q. CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning. J Mol Biol 2023;435:168059. [PMID: 36967040 DOI: 10.1016/j.jmb.2023.168059] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023]
34
Muenks A, Zepeda S, Zhou G, Veesler D, DiMaio F. Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps. Nat Commun 2023;14:1164. [PMID: 36859493 PMCID: PMC9976687 DOI: 10.1038/s41467-023-36732-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023]  Open
35
Burton-Smith RN, Murata K. Cryo-electron Microscopy of Protein Cages. Methods Mol Biol 2023;2671:173-210. [PMID: 37308646 DOI: 10.1007/978-1-0716-3222-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
36
Li J, Rahmani H, Abbasi Yeganeh F, Rastegarpouyani H, Taylor DW, Wood NB, Previs MJ, Iwamoto H, Taylor KA. Structure of the Flight Muscle Thick Filament from the Bumble Bee, Bombus ignitus, at 6 Å Resolution. Int J Mol Sci 2022;24:377. [PMID: 36613818 PMCID: PMC9820631 DOI: 10.3390/ijms24010377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022]  Open
37
Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. Integrating model simulation tools and cryo‐electron microscopy. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
38
Sorzano COS, Vilas JL, Ramírez-Aportela E, Krieger J, Del Hoyo D, Herreros D, Fernandez-Giménez E, Marchán D, Macías JR, Sánchez I, Del Caño L, Fonseca-Reyna Y, Conesa P, García-Mena A, Burguet J, García Condado J, Méndez García J, Martínez M, Muñoz-Barrutia A, Marabini R, Vargas J, Carazo JM. Image processing tools for the validation of CryoEM maps. Faraday Discuss 2022;240:210-227. [PMID: 35861059 DOI: 10.1039/d2fd00059h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Urzhumtsev A, Lunin VY. Analytic modeling of inhomogeneous-resolution maps in cryo-electron microscopy and crystallography. IUCRJ 2022;9:728-734. [PMID: 36381145 PMCID: PMC9634607 DOI: 10.1107/s2052252522008260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
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Zhou W, Yadav GP, Yang X, Qin F, Li C, Jiang QX. Cryo-EM structure-based selection of computed ligand poses enables design of MTA-synergic PRMT5 inhibitors of better potency. Commun Biol 2022;5:1054. [PMID: 36192627 PMCID: PMC9530242 DOI: 10.1038/s42003-022-03991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 09/13/2022] [Indexed: 12/31/2022]  Open
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Tenjo-Castaño F, Sofos N, López-Méndez B, Stutzke LS, Fuglsang A, Stella S, Montoya G. Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon. Nat Commun 2022;13:5792. [PMID: 36184667 PMCID: PMC9527255 DOI: 10.1038/s41467-022-33504-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022]  Open
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Vilas JL, Carazo JM, Sorzano COS. Emerging Themes in CryoEM─Single Particle Analysis Image Processing. Chem Rev 2022;122:13915-13951. [PMID: 35785962 PMCID: PMC9479088 DOI: 10.1021/acs.chemrev.1c00850] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Girbig M, Xie J, Grötsch H, Libri D, Porrua O, Müller CW. Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals. Cell Rep 2022;40:111316. [PMID: 36070694 DOI: 10.1016/j.celrep.2022.111316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 12/20/2022]  Open
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Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion. Commun Biol 2022;5:898. [PMID: 36056184 PMCID: PMC9438360 DOI: 10.1038/s42003-022-03863-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 08/18/2022] [Indexed: 12/18/2022]  Open
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Ramírez-Aportela E, Carazo JM, Sorzano COS. Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools. IUCRJ 2022;9:632-638. [PMID: 36071808 PMCID: PMC9438491 DOI: 10.1107/s2052252522006959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
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Chung JM, Durie CL, Lee J. Artificial Intelligence in Cryo-Electron Microscopy. Life (Basel) 2022;12:1267. [PMID: 36013446 PMCID: PMC9410485 DOI: 10.3390/life12081267] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022]  Open
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Jiménez de la Morena J, Conesa P, Fonseca YC, de Isidro-Gómez FP, Herreros D, Fernández-Giménez E, Strelak D, Moebel E, Buchholz TO, Jug F, Martinez-Sanchez A, Harastani M, Jonic S, Conesa JJ, Cuervo A, Losana P, Sánchez I, Iceta M, Del Cano L, Gragera M, Melero R, Sharov G, Castaño-Díez D, Koster A, Piccirillo JG, Vilas JL, Otón J, Marabini R, Sorzano COS, Carazo JM. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. J Struct Biol 2022;214:107872. [PMID: 35660516 PMCID: PMC7613607 DOI: 10.1016/j.jsb.2022.107872] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 11/25/2022]
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Cryo-EM structures show the mechanistic basis of pan-peptidase inhibition by human α2-macroglobulin. Proc Natl Acad Sci U S A 2022;119:e2200102119. [PMID: 35500114 PMCID: PMC9181621 DOI: 10.1073/pnas.2200102119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
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Wang Z, Patwardhan A, Kleywegt GJ. Validation analysis of EMDB entries. Acta Crystallogr D Struct Biol 2022;78:542-552. [PMID: 35503203 PMCID: PMC9063848 DOI: 10.1107/s205979832200328x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/23/2022] [Indexed: 11/17/2022]  Open
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DeVore K, Chiu PL. Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity. Biomolecules 2022;12:628. [PMID: 35625556 PMCID: PMC9138638 DOI: 10.3390/biom12050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023]  Open
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